@BioDataScience Frankly the right way to do it would have been to assign meaningful read group identifiers (includi… https://t.co/lPwXwITnMu

The #GATK is one of the software packages that benefits from the work of Jose and his team — We’re super grateful f… https://t.co/nw9ZbjoEia

@LoreAment There's an external developer (and hero of the people) who is working on it as a side project. You can s… https://t.co/U0NzCbI3A8

Solutions to Problems

Tips for solving common problems and errors

Allele Depth (AD) is lower than expected
AnalyzeCovariates fails with error message "RScript exited with 1"
Errors about contigs in BAM or VCF files not being properly ordered or sorted
Errors about input files having missing or incompatible contigs
Errors about misencoded quality scores
Errors about read group (RG) information
Errors in SAM/BAM files can be diagnosed with ValidateSamFile
I am unable to use VQSR (recalibration) to filter variants
I do not get the annotations I specified with -A
I expect to see a variant at a specific site, but it's not getting called
I need to run programs that require different versions of Java